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Add ability to set library path via COMPLEASM_LIBRARY_PATH if --library_path unspecified #32

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Add ability to set library path via COMPLEASM_LIBRARY_PATH if --library_path unspecified #32

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39 changes: 28 additions & 11 deletions compleasm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -73,8 +73,12 @@ class Downloader:
def __init__(self, download_dir=None, download_lineage=True, download_placement=True):
self.base_url = "https://busco-data.ezlab.org/v5/data/"
self.default_lineage = ["eukaryota_odb10"]
if download_dir is None:
self.download_dir = "mb_downloads"
if download_dir == None:
library_path_env = os.getenv("COMPLEASM_LIBRARY_PATH")
if library_path_env is None:
self.download_dir = "mb_downloads"
else:
self.download_dir = library_path_env
else:
self.download_dir = download_dir

Expand Down Expand Up @@ -2634,9 +2638,10 @@ def main():
download_parser = subparser.add_parser("download", help="Download specified BUSCO lineages")
download_parser.add_argument("lineages", type=str, nargs='+',
help="Specify the names of the BUSCO lineages to be downloaded. (e.g. eukaryota, primates, saccharomycetes etc.)")
download_parser.add_argument("-L", "--library_path", type=str, default="mb_downloads",
help="The destination folder to store the downloaded lineage files."
"If not specified, a folder named \"mb_downloads\" will be created on the current running path.")
download_parser.add_argument("-L", "--library_path", type=str, default=None,
help="The destination folder to store the downloaded lineage files. "
"If not specified, the environment variable COMPLEASM_LIBRARY_PATH is used. "
"If that is not set, a folder named \"mb_downloads\" will be created on the current running path.")
download_parser.set_defaults(func=download)

### sub-command: list
Expand All @@ -2652,8 +2657,10 @@ def main():
protein_parser.add_argument("-l", "--lineage", type=str, help="BUSCO lineage name", required=True)
protein_parser.add_argument("-o", "--outdir", type=str, help="Output analysis folder", required=True)
protein_parser.add_argument("-t", "--threads", type=int, help="Number of threads to use", default=1)
protein_parser.add_argument("-L", "--library_path", type=str, default="mb_downloads",
help="Folder path to stored lineages. ")
protein_parser.add_argument("-L", "--library_path", type=str, default=None,
help="Folder path to stored lineages. "
"If not specified, the environment variable COMPLEASM_LIBRARY_PATH is used. "
"If that is not set, a folder named \"mb_downloads\" on the current running path will be used.")
protein_parser.add_argument("--hmmsearch_execute_path", type=str, default=None, help="Path to hmmsearch executable")
protein_parser.set_defaults(func=protein_fun)

Expand All @@ -2678,8 +2685,10 @@ def main():
analysis_parser.add_argument("-l", "--lineage", type=str, help="BUSCO lineage name", required=True)
analysis_parser.add_argument("-o", "--output_dir", type=str, help="Output analysis folder", required=True)
analysis_parser.add_argument("-t", "--threads", type=int, help="Number of threads to use", default=1)
analysis_parser.add_argument("-L", "--library_path", type=str, default="mb_downloads",
help="Folder path to stored lineages. ")
analysis_parser.add_argument("-L", "--library_path", type=str, default=None,
help="Folder path to stored lineages. "
"If not specified, the environment variable COMPLEASM_LIBRARY_PATH is used. "
"If that is not set, a folder named \"mb_downloads\" on the current running path will be used.")
analysis_parser.add_argument("-m", "--mode", type=str, choices=["lite", "busco"], default="busco",
help="The mode of evaluation. dafault mode: busco.\n"
"lite: Without using hmmsearch to filtering protein alignment.\n"
Expand Down Expand Up @@ -2708,9 +2717,10 @@ def main():
run_parser.add_argument("-t", "--threads", type=int, default=1, help="Number of threads to use")
run_parser.add_argument("-l", "--lineage", type=str, default=None,
help="Specify the name of the BUSCO lineage to be used. (e.g. eukaryota, primates, saccharomycetes etc.)")
run_parser.add_argument("-L", "--library_path", type=str, default="mb_downloads",
run_parser.add_argument("-L", "--library_path", type=str, default=None,
help="Folder path to download lineages or already downloaded lineages. "
"If not specified, a folder named \"mb_downloads\" will be created on the current running path by default to store the downloaded lineage files.")
"If not specified, the environment variable COMPLEASM_LIBRARY_PATH is used. "
"If that is not set, a folder named \"mb_downloads\" on the current running path will be used or created.")
run_parser.add_argument("-m", "--mode", type=str, choices=["lite", "busco"], default="busco",
help="The mode of evaluation. dafault mode: busco.\n"
"lite: Without using hmmsearch to filtering protein alignment.\n"
Expand Down Expand Up @@ -2741,6 +2751,13 @@ def main():
sys.exit()

args = parser.parse_args()
# if --library_path unspecified, check COMPLEASM_LIBRARY_PATH. If unset, use "mb_downloads" as default
if args.library_path == None:
library_path_env = os.getenv("COMPLEASM_LIBRARY_PATH")
if library_path_env is None:
args.library_path = "mb_downloads"
else:
args.library_path = library_path_env
args.func(args)


Expand Down